rs16894458

Variant names:

• chr5-61740609-T-A
• rs16894458
• ENST00000507461.2:n.140-7993T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507461.2(LINC03122):​n.140-7993T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,298 control chromosomes in the GnomAD database, including 573 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.064 (573 hom., cov: 32)
• Consequence: LINC03122 ENST00000507461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 2 publications found

Genes affected

LINC03122 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507461.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03122	ENST00000507461.2	TSL:4	n.140-7993T>A		intron	N/A
	LINC03122	ENST00000655479.2		n.149-7993T>A		intron	N/A
	LINC03122	ENST00000656556.1		n.113-7993T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9668 AN: 152180 Hom.: 566 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0522

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0637 AC: 9699 AN: 152298 Hom.: 573 Cov.: 32 AF XY: 0.0648 AC XY: 4828 AN XY: 74474

African (AFR) AF: 0.133 AC: 5530 AN: 41540

American (AMR) AF: 0.0772 AC: 1181 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.0889 AC: 461 AN: 5186

South Asian (SAS) AF: 0.154 AC: 743 AN: 4826

European-Finnish (FIN) AF: 0.0138 AC: 147 AN: 10622

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0203 AC: 1382 AN: 68036

Other (OTH) AF: 0.0521 AC: 110 AN: 2112

Alfa AF: 0.0447 Hom.: 38

Bravo AF: 0.0701

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.2
DANN	Benign	0.79
PhyloP100		0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16894458;

hg19: chr5-61036436;

COSMIC: COSV72696654;